Raise your feeder and waterer up on something. They will still get some shavings in them, but not as bad. Ideally, the basin of the feeders and waterers should be level with the smallest chicks back. You'll need to continue to raise them as the chicks grow. In my coops of adult and nearly adult chickens, the waterers are up on cinder blocks and the feeders are hung.

I made a platform out of 2x2s and half-inch hardware cloth to put my brooder waterers and feeders on. When they are big enough I put the platform on blocks made of pieces of 2x4s to raise it higher still. Keeps them from getting so many shavings in the water and if they should somehow manage to spill it they can't get into the wet bedding.